TRON: New Frontiers
by Azaelynn
Summary: The world wasn't ready for Flynn's miracle. When circumstances force Sam back into the Grid, alone and trapped, how will he cope when once he's finally released, the world he knows is gone? Will he be able to find a kindred soul in Jim Kirk?
1. Chapter 1

TRON: NEW FRONTIERS

LADY SHINIGAMI2

DISCLAIMER: I'm only borrowing them to play with a while...

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><p>CHAPTER 1<p>

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><p>Fuck this shit! It wasn't to happen like this! Another bullet slammed into the brick wall beside him, pelting him with minor debris as he and Alan ran through alleyways and side streets, hoping desperately to lose the hunters after them, dodging bullets as they went. Beneath the desperation of their situation, he felt a mild relief that they were wanted alive rather than dead.<p>

He leapt over a chain link fence, pausing only long enough to help Alan over before the older man grabbed his wrist, dragging him into a ridiculously narrow hole in the wall, ducking into a derelict doorway just moments before the black ops assassins chasing after them ran past their unlikely refuge.

Alan remained motionless for several long minutes, barely breathing as he kept a hand over Sam's mouth before dragging him further into the darkness of the alleys, twisting through the maze until, finally, Sam recognized where they were, and he moved forward past his mentor to unlock one of the side doors to the old arcade, where everything started.

It was dark inside, dusty plastic sheets still covering the machines, and windows covered in dirt and grime, just as he had left it a year and a half ago, after his first and last visit to the Grid. It looked like nothing had been disturbed since then, and for that, Sam was relieved. They could hide here for a time.

It was one of the last places they had to run to.

Alan kept them away from the covered windows, sticking to the inky shadows, and Sam was still stunned that the older man was still with him, helping him get away and survive. Not that Sam ever doubted Alan's support; he just hadn't been expecting his mentor and surrogate father figure to be so fit and so quick! The man was in ridiculously good shape for his age!

He was also more sneaky than Sam had anticipated.

At any other time, the ninja abilities would be freaking him out by now, but Sam didn't have time to freak out, not with the damned government on his ass.

It had been such a mistake, everything, all of it. The world wasn't even near ready for his dad's miracle, and now it was gone. Quorra was dead, one of the first to die after Dillinger's coup.

He still wasn't sure how that slimy bastard had managed to hack through his security and find his files on the Grid or Quorra's genetic make-up that allowed him to a foray into the realm of bioengineering and medicine. Quorra had allowed them to make great advancements in everything his father had told him about (bio-digital jazz, man), in only a few short months, and now she was gone.

Sam didn't think he'd ever forget the sight of her sightless eyes staring at him, blood dripping from the bullet hole in her forehead.

That had been only yesterday, although it felt like so much longer. He wasn't really sure how much longer he and Alan would be able to keep running.

"Sam, show me how to get down to the lab." Alan's gravelly voice cut through his reminiscence and Sam blinked, focusing back on reality. This wasn't the time to lose himself in his own head, he had to keep his focus. He led Alan to the ancient Tron console, shifting it out of the way to reveal the hidden door he'd stumbled on, opening it to show his mentor the stone staircase going beneath the building.

Alan stared into the darkened stairway, almost indistinguishable from the gloom of the abandoned arcade they stood in. The older man nodded once, eyes cutting to glance around them sharply, and Sam could almost hear the gears turning in his surrogate father's head as he planned.

"Alan?" It was barely a whisper, but his voice seemed far too loud. "What are you thinking?"

"Help me unplug all the machines. After that, we're turning the power on."

Confused, Sam frowned but he moved to comply with Alan's orders, confident that the man knew what he was doing. He trusted Alan with his life, literally, this time, and if Alan was prepared to risk possible detection to bring about whatever it was he was planning to save their asses, then he would obey without question.

It only took them about an hour to secure the building so that anyone looking in from outside couldn't tell that the place was even wired for electricity, so when Alan flipped the switch in the switch box, there was only a very hum, barely audible in the gloom surrounding them.

"When you told me about the Grid, you said your father explained that time moved differently there, that hours spent in the Grid was only minutes here." Alan moved towards the back of the building, opening a fairly hidden door to reveal a supply closet. He started digging around in it, and Sam could only stare, confused. He had no idea what the other man was planning. "The computer he used down in the lab was pretty advanced considering its age, which doesn't surprise me."

"Where are you going with this, Alan?"

"Can you use the computer down in the basement to reverse that aspect of the Grid? Make it so that hours here is only minutes there? Seconds, even?"

An idea, a suspicion, warily crept into Sam's thoughts, but he couldn't reason it out yet, not without more information from his mentor. "Maybe, um, probably. I managed to bring the time difference to a more equal footing within my first couple of months at Encom."

"Good. Head down and get started. I'll finish things up here and keep a watch out."

"Seriously, Alan, what's the plan?"

Sam had already started for the secret entrance of his father's lab, but he froze as Alan met his gaze squarely, the steel in his eyes sending a shiver down his spine.

"You're going back to the Grid."

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><p>AN: New idea that kinda hit very vividly, so we shall see where this goes. This absolutely DEMANDED to be written, much to the dismay of my regular readers, I'm sure, who are waiting for me to update my other stories. Still working on it, guys, but please let me know what you think of this!


	2. Chapter 2

TRON: New Frontiers

Disclaimer: Only borrowing them... I can't keep them... damn...

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><p>Chapter 2<p>

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><p>Alan didn't say anything more about his plan, but Sam knew there was definitely more to it than just sending Sam back to the Grid. Yes, he hadn't missed Alan's focus on just him in the Grid, but he couldn't figure out what the older man planned for himself, or anything else, for that matter.<p>

Staring at the older man for a few moments longer, Sam broke eye contact first, quickly descending into the pitch black of the hidden basement where his father's lab was waiting for him. He had to trust Alan; he knew that, even if the lack of knowledge made him uneasy.

The room containing the laser and his dad's computer was very dimly lit by the light that barely filtered through the dirty and tiny window situated above the computer, so his first task was to cover it up. He found an old blanket on the tattered and sagging couch, folding it double before duct-taping it over the window, cutting off the dim light.

He flipped on the light switch by the door and turned the large computer back on, waiting patiently as the monstrosity booted up. While he waited, Sam inspected the laser, and remembering how he stumbled onto the Grid in the first place, he unplugged the damned thing so as to not accidently activate it again while he was busy modifying the source code of the Grid.

Programming was so easy for him, and he uploaded the data back onto the computer from the tiny chip that had hung around his neck for the last year and a half. Before, when he had only been looking around the system for curiosity's sake, he hadn't really tried to actually hack the system, but now, with everything that was at stake for both him and Alan, he concentrated his efforts into his hacking skills, and once he was in, he quickly lost himself to the programming, mind racing as he worked to identify the code that would allow him to alter the way time flowed in the Grid.

He lost his sense of time as the hours passed, code flying across the open command windows and flitting through his mind as he mentally processed the math and the physics, theories and calculations forming almost faster than he could type the input commands.

While he worked on the time equation, Sam also fixed the broken code within the Grid as he happened upon it, erasing and rewriting program functions, removing irreparably corrupt data and creating new data to replace it. He found in the digital map where the entry point was and decided to build a new portal there, in the Grid's version of the arcade, for simplicity's sake. The Grid had been damaged, he knew, by the explosion of the portal after his father and CLU had re-integrated, but with time, it would be modified and made anew.

Sam honestly had no idea how much time had since he first started working on repairing the Grid and reversing the passage of time within the Grid, but when he finally leaned back in his chair and stretched out sore and aching muscles, his spine popping as he moved, he breathed a heavy sigh of relief.

He'd done it. He couldn't be 100% positive, not without entering the Grid again, but he was sure he'd fixed the time dilemma. If everything went the way it should, for every second that passed in the Grid, five hours would pass outside the Grid. With the portal right in the other side's version of the arcade, Sam would only be waiting a few seconds, maybe a few minutes at most, depending on how long it took Alan to get them safe or get the government to back off. Any longer than a few minutes, and Sam would know that something had gone wrong while he was stuck in the Grid.

When he thought about it, the prospect of potentially getting trapped in the Grid absolutely terrified him.

He would just have to continue to trust in Alan.

He stood slowly from his chair, cracking his neck as he did, running a hand through his hair to rub at the base of his skull, in an attempt to ease the ache he felt there. Habit had him looking around for a clock, and he shook his head ruefully. There wasn't any point; any clock down here would have died years ago.

He decided to look for Alan, to give the good news on the Grid, and to also offer his assistance should the older man need it. He was also a little worried, cautious just on the off chance that something had happened while he had been preoccupied. If that was the case, he deserved to be caught by their pursuers and that sent an arrow of deep, sharp shame to his gut.

He crept up the stone steps cautiously, peeking around the corner as he reached the main floor of the arcade, but the place was as quiet as when they'd arrived, and Alan was nowhere in sight. A glance towards the grimy windows revealed that the sun had long since set, leaving Sam with the impression that he's been sequestered in the laser lab for at least six hours, maybe a little longer, since he didn't actually have any idea what time it was.

Creeping around the silent machines, Sam headed towards the back of the arcade, to the set of stairs leading to his father's office. He vaguely remembers hearing stories from when he was a kid about his dad used to live here before his rise at Encom. Somehow, those old stories don't surprise him.

He could just barely see the smallest hint of light peeking out from under the door at the top of the stairs, and he wonders again at just what, exactly, Alan is planning. It kind of scares him, just a little bit, since he has the vague feeling that they're setting up for a final showdown, or something.

"Alan?"

"In here, Sam." He frowned slightly, hearing exactly how tired Alan would deny he was. Sam pushed open the door, unprepared for the sight before him, a veritable disaster zone, with Alan calmly in the middle. There were cleaning chemicals from the supply closet downstairs, pieces of what looked like an old computer, bits of wire, the whole mess was everywhere.

"What are you doing?"

"Making a bomb. Just a few small ones, just in case."

Sam stared in surprise at his mentor, his mouth hanging open as he struggled to process this new information. There were those damn ninja skills again.

"A bomb? Why? What could we possibly use a bomb for?"

Alan tossed a smirk his way, clearly enjoying Sam's surprise. "Just a contingency plan, just in case. The ones I'm making will blow with enough destructive force to collapse a building about the size of the arcade."

"Ok, I still don't see why we need a bomb, of all things, but I'll take your word for it. Good news, though; I finished recalibrating the Grid. For every second that passes in there, five hours will out here. That should be plenty of time for whatever you're planning, which I still have no clue on, by the way, and can I just say that what we're doing right now, here, feels a bit too much like a final stand for my tastes."

Alan's face didn't change, but his expression did take on a sombre feel, something in his eyes silently confirming Sam's words. "That's because it might be, Sam."

"Why?" He hated how weak he sounded, and he hated how his eyes started misting over, causing him to blink.

"The world's not ready for you, or the Grid. People are selfish, Sam, and that won't change in either of our lifetimes, so I'm making sure that you survive long enough to do something truly special. You deserve this, Sam, and I wish that I could be there with you when it happens," At this point, Sam started crying softly, unable to hold back the tears.

"Alan, I – I don't want to lose you, too," he hung his head, tears spilling down his face to drip down onto the dusty floor. Suddenly there were arms wrapped around him and he returned the embraced, clinging to his surrogate father, the only man who'd bothered, who cared enough.

"It'll be ok, Sam. I promise."

They stood there, wrapped in each other's arms, unwilling to break the mood. Alan had been his father in every sense but blood, taking care of him after Kevin Flynn disappeared, and now there stood the very real possibility of losing that support very soon.

It takes him a while, but Sam's able to compose himself, wiping away the evidence of his insecurity and fear, because holy shit, this was way out of his comfort zone. He smiled, well, tried to anyway before moving back down the stairs, looking over his shoulder to Alan.

"So," his voice is still a little shaky, but he ignores it. "Want to see my mad programming skills?"

Alan grins at him, allowing him to lighten the mood. "Sure, let's see what chaos you've created, and I can show how a real programmer works."

"Ow, that's hurts, man. That really does."

Back down in the lab, Sam brought up the different screens he'd been working with, pointing out all the details to Alan, all the adjustments and repairs he'd made to the system, and when Alan started making suggestions, small things really, like a small armoury right by the portal for his use on the off-chance Sam encountered hostile programs, he eagerly implemented them, fingertips flying across the keyboard, the small room silent save for their whispered conversation.

It was about an hour, maybe two hours later, when Alan froze midsentence, staring at a section of scrolling code on one of the five screens Sam had up.

"I know this code," he pointed to a specific piece of code. "Can you pull up the program that this originates from?"

Sam shrugged, already searching it out. "Sure, it'll just take a sec."

He wasn't at all prepared for the name of the program when he found it, though.

Alan had found Tron.

"Sam, move, please." He eagerly relinquished his seat to the older programmer, watching in awe at the speed his mentor displayed as he pulled the original program file to an isolated repair screen, tracking the corrupted data that Sam knew came from CLU, but it didn't stop Alan from reformatting certain parts of the corruption, repairing what he could without erasing Tron's memory files and essentially creating the security program from scratch.

"You told me about the corruption, the reprogramming CLU did, but I didn't think it would be this bad. I can't repair all of it, not without losing everything he is now, but maybe you could help him from the inside." Alan barely spared him a glance as he continued to work on his best creation. "I can't get rid of all the Rinzler aspects, they're too ingrained."

"It's ok. If there's time, I'll try to help him."

They closed down all the different repair screens and windows, turned on the laser, and left only the laser activation command up and waiting. Sam realized that they really couldn't put it off anymore.

It really, fucking terrified him.

Alan seemed to sense his hesitation and stood, stretching a bit before going back up to the main floor, Sam following right behind him. Together, they grabbed the makeshift bombs, and according to Alan's directions, placed them strategically around the arcade, by the front door, behind several of the arcade machines, and in the office. Alan had it planned that if, or rather when, the bombs went off, the building would collapse, probably destroying the basement stairs, but leaving the lab itself intact.

Then there was nothing left but to send Sam back to the Grid.

Alan stayed outside the laser room, pulling Sam into a bone-crushing hug, arms wrapped around the man he'd practically raised as his own, tearing up at the feel of Sam's arms around his waist, clinging to him just as tightly.

"You survive, you hear me? No matter what happens, I want you to keep going, because you're so special, Sam, and you're going to change the world." He whispered, barely suppressing the emotions he felt broiling just beneath the surface.

Sam choked, trying to draw in breathe to respond and failing, his throat closing up as tears slid fresh down his face, soaking into Alan's collar. "I hear ya. I promise."

"You just go through that door and don't look back, don't hesitate."

"I won't."

"I love you, Sam. You're my son in all but blood, and I love you, I'm proud of you."

Sam cried harder, his body quaking in Alan's embrace. "I love you, too, Alan."

Alan held him like that for a while, pulling away once the shaking stopped and with a sad, agonized smile, he wiped away the tears from Sam's cheek. "Goodbye, Sam Flynn."

Sam nodded shakily, taking a step back away from his surrogate father. "Goodbye, Alan Bradley."

No, that didn't seem quite right. "Goodbye, Alan_1."

Alan managed a smirk at that. "Take care of Tron for me."

Sam nodded again before turning his back on Alan, keeping his promise to not look back, closing the door to the lab behind him.

With a heavy, world-weary sigh, Alan bolted the padlock, pocketing the keys before returning to the main floor of the arcade to grab the detonator for the bombs and the old rifle he knew Kevin used to keep in the upstairs office, remembering old stories of his friend fending off potential robberies back in the day. He was vaguely surprised to see a pistol as well, but he grabbed it as well, doing a quick weapons check to ensure they were functioning before settling down at the back of the arcade to wait.

Turns out he didn't have to wait very long. He knew their pursuers would have eventually found the arcade, but since it had been derelict for about twenty years now, he couldn't fault them for taking this long.

They tried taking a silent approach at first, gently easing the front door open, and if Alan hadn't been as vigilant, he might have missed it in the early morning hours. Instead, he crept closer to the Tron console, raising the rifle to take aim, sliding the barrel between two of the taller games to give him some semblance of cover.

He waited until he knew the whole squad was in the arcade, all six of them, slowly spreading out along the perimeter before taking his shot. He fired rapidly, emptying the rifle before the soldiers could react, killing or fatally wounding two of the bastards. He bolted as returning fire was shot, destroying the games around him, but he kept his wits on him, swinging the rifle and catching a third that had been sneaking up on him, dropping him to land in a heap at his feet.

The remaining three soldiers were already on him, weaving through the game machines to get closer, firing their weapons as Alan dashed for the still open entrance to the basement, bringing up the pistol to shoot back.

He slammed into the back of the machine as a bullet tore through him, burning white-hot, tearing a scream from his throat. Despite feeling blood already pouring from the bullet wound, Alan was able to shoot another assassin point-blank in the face, as a few more bullets buried themselves in his body.

Dizzy from blood loss, Alan was aware he only had minutes left, so he sealed himself in the basement stairs, nearly falling down them. He'd sealed the door on his side, giving him enough time to stagger down the stairs, leaving a thick trail of blood as he went. He collapsed at the door leading to the laser, leaning against the wood as his life leaked slowly from his body.

He had very little time left. He couldn't fail Sam now.

He dropped the pistol and grabbed the detonator in shaking hands, fumbling slightly before pressing the button, grinning weakly at the explosions going off upstairs. Just as he predicted, the main stairway into the basement collapsed, but only dust trickled down from the ceiling where he was.

He didn't mind that this place would become his tomb.

Sam was safe, and that's all that mattered.

Someone would find him again, Alan knew it, but it would be years from now, and maybe then, the world would be ready for Sam and the change he would bring.

He was so tired.

His breathing was growing shallower, so it wasn't long now.

Sam was safe, so he could rest now.

Alan smiled as his eyes drifted shut.

So tired, but that was ok.

_Kevin, you would be so proud._

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><p>AN:there's gonna be another chapter of solely Tron!verse before we get to the crossover bit, but please, don't hesitate to review! I want to know if i'm handling this fandom well, since this is my first forray into Tron. Also, I almost cried a few times while this chapter, so please a review if i did well. Thanks, and until next time!


	3. Chapter 3

TRON: New Frontiers

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><p>UPDATE: I have come to the realization that I will be needing a beta reader soon, preferably someone with some knowledge of computers and programming, in order to finish the next chapter, and to help me in general with plot holes and stuff. If anyone is interested, please send me a PM, and I will get back to you as soon as I can.<p>

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><p>Chapter 3<p>

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><p>It was unbelievably hard to not look back as he walked into the laser lab, closing the door behind him, but Sam had promised Alan that he wouldn't, that there'd be no hesitation, and he'd be damned if he broke his word now.<p>

He only faltered once, leaning against the closed door that was his only barrier from the man who had taught him everything he knew, had taken the time to give a damn when no one else had ever bothered.

He sighed, focusing on the task at hand, since this still terrified the crap out of him. The way he had it figured, he had about five hours, once inside the Grid, before he could legitimately start worrying that something on this side went horribly wrong, but the point of no return would be about ten hours in the Grid, because that would be approximately twenty years on this side.

Any more time than that, and Alan would more than likely be dead, and he would have to trust in a random stranger to stumble across him. He _really_ didn't want to leave that to chance, but he didn't exactly have a choice.

No hesitation. He'd promised Alan. He'd go back to the Grid, and he would survive, and he would change the world, for Alan's sake.

Even though he had no idea how he was going to make that happen, but still, it was the principle of the idea.

He sat down in front of the laser, stared at the activation screen for a moment before hitting the keyboard, activating the damn laser and before he could blink, he was in the Grid, the ride just as fast as that first time, jolting his senses.

Sam braced himself against the desk, breathing deeply to calm his racing heart, before looking around at the achingly familiar room. Black and sleek, with white circuitry giving off minimal light, and out the small window, he could see lightning crackle across the thin strip of digital sky.

Looking down at himself, Sam wasn't surprised to see the jumpsuit and armour he'd worn the last time he'd been here, and he was comforted by the weight of his identity disk on his back.

Well, a few seconds had already passed and no message from Alan. He forced himself not to panic; he knew it could take a while before they were safe. In the meantime, he had work to do.

In the other room of the virtual basement, Sam found the portal he'd created, looking kind of like a teleportation pad from those old sci-fi TV shows about space explorers he'd watched as a kid. There was a small console next to it, designed to act as a means of communicating with the outside world, which would let him know when he was going home. He was supposed to wait until Alan contacted him.

Next to the pad was the armoury Alan had suggested, filled with rifles and other assorted equipment, from guns to shields to swords. He strapped an energy shield to his wrist; the shield part currently deactivated, but would be large enough to protect him from most things on the Grid. He belted a gun holster around his waist, the weight of the firearm surprisingly comfortable on his hip and he also attached one of the energy swords on the opposite side, the weapon itself strongly reminding him of lightsabers, but then again, he _was_ that big of a geek at heart and wasn't really surprised.

Sam finished arming himself by slinging a rifle over one shoulder before going upstairs to the front of the arcade, carefully looking out one of the windows to try and get a feel of the situation outside.

The streets were deserted on street level, but the surrounding buildings had taken some damage since he was here last, and in the sky, there were a few light jets flying high, and Sam could also see some Recognizers, too. There were definite signs of battle. Either way, it probably wasn't a smart idea to leave his current location, but he would have to if he wanted any information at all about what's been happening in the Grid since CLU's reintegration with his father.

Or maybe...

He was a User, one that had extensively reprogrammed the Grid, fixing it and getting rid of some of the corruption. His father, Kevin Flynn, was the first to come down here, and as The User, the Creator, Flynn had been in control of power, a lot of raw power. Kevin Flynn had been able to create programs and functions and systems commands effortlessly while still inside the Grid.

What was stopping Sam from being able to do the same thing?

How to go about doing that, though? Was he able to just create Programs here?

Why not? He'd give it a shot, since he was more than a fair hand at programming, so his first order of business should be creating an ally for himself, someone to help him here.

Decision made, Sam fled back down to the basement, and on the wall opposite of the portal, he ran his fingers along the glowing circuits, pulling up digital readouts and holograms of the building, moving code around to create another room, almost isolated from the rest of the Grid and buried beneath the building's code, making it invisible to outsiders. No one would be able to find this room unless they were looking for it and knew where it was.

Passing through the glowing new door, Sam smiled; delighted at seeing the creative space he would need to work. The room was almost pitch black, only throwing off dim blue illumination from the hexagonal patterns in the floor, the ceiling and the walls. The room itself wasn't terribly large, only eight by ten feet around, but it was all the space he needed.

He knelt down to one knee, laying his right palm flat on the surface of the floor, activating the neural interfacing and with a few thoughts; an adult sized incubation tube was raised, a humanoid shell already floating inside. This was his base, his blanket Program, ready for him to build upon.

First, what did he need in a Program? Since he needed information, a hidden search function was necessary, for more subtle inquiries. A backup security function for self protection. Some administrative functions, a basic but adaptable operating system, an advanced encryption setting to prevent hacking, even if the program was captured by other hostile programs. Anything he could think of, he wrote the code for his program, creating what would be his most trusted ally.

A quick look at the incubation tube had Sam doing a double take. The damned thing looked like he could pass for his twin! Shit, that was bad, that wouldn't do at all. He turned his attention back to the interface he was using, digging through the data to try and change the program's appearance. He found what he needed and tweaked it, changing the shape of the face, and darkening the hair and eyes, and he double checked the tube again, this time content, since he didn't immediately associate the program currently incubating as Sam Flynn's twin.

The whole thing gave him an idea for a name for his program, though. Decided, Sam finished writing the code and closed the interface, unlocking the incubation tube as he did. He stood on his feet, observing his creation as the program took his first steps as a living, fully functioning being.

He was Sam's height, and same body type, which was currently covered neck to toe in suit similar to Sam's, but the armour was different, more solid, with more circuitry glowing a bright blue. His dark eyes were partially shielded with a visor, similar to one Jarvis, that spineless program that had followed CLU, had sported, but it looked way cooler now.

"Do you know who you are?" He asked, wanting to see if he'd done this right. It was his first time writing a program inside the Grid, which was totally different than looking at a computer screen with scrolling text.

The program nodded briskly, with no hesitation. That was good. "Yes, I am Gemini. How may I be of assistance?"

His voice was different from Sam's, deeper, if a bit flat. That was also good, even though he didn't think any hostile program would be able to recognize him from his voice. "For now, you can help me fortify this place. This building needs to be secured properly before we do anything else, like sending you out on a reconnaissance mission."

Gemini nodded once, following Sam as he left the basement, waiting patiently for his orders. Sam looked around at the empty space of the arcade, so similar to its outside-Grid counterpart, but lacking all the machines that he was used to.

"Gemini, can you take care of the windows, to start with? I want them reinforced to withstand a substantial amount of damage, and upgrade the walls if you have to, to support the changes. I also want them tinted; we can see out, no one can see in. Got it?"

The program nodded. "Yes, sir. Right away, sir."

"And if you need to, just call me Sam, ok?"

Gemini frowned at him. "But you are my Creator. Is it not a sign of disrespect to address you so informally?"

Sam grinned at him, shaking his head. "Not really, I actually prefer the informality. Plus, no one can know that I'm your Creator, or that I am a User. It's very dangerous for Users right now."

Gemini nodded. "I see. I trust in your judgement."

He then proceeded to the closest window, without coming into view from the outside, and with some of the administrative functions Sam had given him, pulled up an interface and started meddling. At least that's what Sam called it, since he wasn't actually right there to see what Gemini was doing, but already, the windows were looking sturdier, stronger, and Sam couldn't help but smile.

This time, he'd done good.

He looked around the empty building again, wondering what else he could do secure this place, and he shook his head, taking in the upstairs room that had been, outside the Grid, his father's arcade office and one-time home. Actually, that was sounding like a good idea, since he'd been running on little more than adrenaline since hearing the gunshots and finding Quorra's body... only yesterday.

Exhaustion was starting to hit him at that realization, and Sam knew he didn't have very long before he collapsed, and there was still so much work to be done. Shaking his head to clear it, Sam headed for the upstairs room, fortifying and concealing the door leading to it; he began to work on making this space liveable, since he was here until further notice.

Equipping the space with a bed, lighting, a small table and a chair was easy, and it was hard to leave the room when he was finished, the growing need to just crawl into bed and either sleep for a week or just weep was so tempting.

Sam knew he was feeling a little numb from everything he'd been through in the last day or so, and the longer he stayed here, the more worried he was that something had happened to Alan. So far, he was refusing to let everything overwhelm him, at least until he was safe and Gemini was able to keep watch, but the inevitable breakdown was getting closer. He would just have to deal until then.

Back down in the main arcade space, Sam allowed himself a small smile at the visible progress he could see, generated from Gemini's efforts with the windows and walls. Gemini was the best program he'd ever written, and it was showing.

"Hey Gemini, how's the upgrading going?"

"I'm about finished here, sir. This building should be the most secure in the sector."

"Excellent, that's great news. Finish up here, and could you go down and check the comm. console for any messages? Also check for me how long the portal will remain open for." At his words, Gemini nodded; closed up the interface he was using and disappeared down into the basement.

At least the program was efficient. They'd work on personality later.

The only thing Gemini hadn't taken care of up here was the door leading out to the street, so Sam decided to reinforce it himself-

A low, rumbling, dangerous growl froze him in place, chills creeping up his spine. He knew that sound, felt the phantom hum of a glowing disc at his throat, remembered being pinned by the weight of the program that sound belong to.

"...User."

Sam spun, pulling out his own identity disc and ready to defend himself, but he wasn't prepared for the sight before him. Rinzler, in all of his imposing glory, was slumped against the doorway of the arcade, armour scuffed and dirty, one arm hugging his side, and Sam could just barely see slowly derezzing code, flaking away piece by piece like embers. What circuitry was visible with the armour was flickering between the dangerous, deadly red glow he knew and was already familiar with, and the bright blue from his childhood stories. His face was still hidden from view by that glossy black helmet.

Now, Sam had long ago figured out that Rinzler was, in fact, Tron but repurposed by CLU. Still didn't make him any less dangerous, even if he was hurt. But Alan's request, echoing through his mind, had him lowering his disc as he looked over the damaged program before him.

"Who are you? CLU's puppet, Rinzler? Or the best security program around, Tron?" Before he started fulfilling Alan's request, he needed this question answered.

The low growl coming from the program hadn't ceased, but Sam was starting to think it was subconscious at this point. The silence hung between them, just bordering on uncomfortable, and as Sam waited for Rinzler's response, he was aware of Gemini standing behind him at the top of the stairs to the basement, keeping still. He could only hope his program followed his lead.

"...User...fight..." Rinzler took a step further into the building, a step closer to Sam, and nearly fell to his knees. "... Fight... for the Users." Another staggering step forward. "...Who am I?"

"Gemini!" His command had his program at his side as Sam lunged for Tron, both of them supporting the injured program's weight between them as they guided him to the living space Sam had constructed. "Go, I'll take care of this; you go seal that door, and set up some alarms too."

Then Gemini was gone, out of the room to complete his task, leaving Sam alone with a severely wounded Tron. With an analytical eye, Sam catalogued all the visible injuries crippling the security program, the most critical being the derezzing gash in his side, but there was also something wrong with his leg, and now that he was closer, Sam could all too clearly see the large crack in the helmet shielding Tron's face from view.

He carefully turned the program onto his uninjured side, removing the dual identity disc from his back, and with a few rhythmic taps to the disc, Sam was able to bring up the equivalent of Tron's DNA, the damage to the program glaring at him, right there to be fixed. Remembering how his father had regenerated Quorra's arm his first time in the Grid, he tried to do the same thing, isolating the damage, deleting it and rewriting new code to fit seamlessly within the double helix of the digital DNA. He also scrolled through the rest of the data, repeating the process with as much of Tron's injuries as he could, he also activated the program's maintenance functions, which had been shut down by what looked like an overload to the system.

There were still a few pockets of corruption, nothing overly critical, but too closely ingrained with Tron's essential system functions for Sam to try and repair it himself. These pockets were probably what Alan hadn't been able to repair, and he was sure that Tron would just have to come to terms with those aspects of Rinzler, but he would try to help where he could.

Finished with Tron's repairs, Sam returned the security program's dual disc to his back, watching as stasis set in and the repairs began to manifest physically, circuits glowing a bright blue as the damage slowly began to heal.

His exhaustion was seriously catching up with him, like, _now_. Tron was currently taking up his bed, though, and he really wasn't sure he could keep his eyes open long enough to create another one. He sat down on the floor beside the bed, leaning against it, and somehow comfortable with Tron right above him.

Sam was brought out of his sleepy daze when Gemini came into the room, staring at him with concern and a small frown. The program knelt down to his level in front of him, one hand on the floor. "Sam, you are in need of rest."

Sam grinned at his creation. "Can't argue with that."

"Sleep. I will keep watch. There were no messages from the portal, but I will wake you should any come through." Gemini said, concern coloring his voice. Seems that personality was beginning to manifest on its own, that was good. Gemini was adapting.

"Sounds good," Sam nodded, blinking to keep his focus on Gemini for just a few more minutes. "It's been a couple hours since I arrived in the Grid, there should be a chronometer in the comm. with a countdown until the portal closes on this side. Wake me when it does, if I'm not up already. Tron should be up in a few hours, keep him here, and I want you to go out into the city on a recon mission. I shouldn't need to tell you to be careful."

Gemini nodded, acknowledging his commands. The program was smart, he'd do fine.

Sam allowed his eyes to close shut as Gemini left the room, leaving him alone with a regenerating Tron, and he couldn't help but feel safe, the quiet rumbling from Tron's helmet lulling him to sleep, and he finally let go and allowed himself to drift off.

* * *

><p>He jolted awake, panting for air as he sat up, disoriented. His dreams flashed through his head, bright vivid images of Quorra, smiling brilliantly one minutes, eyes dead the next. Alan beside him in Encom's boardroom, smiling as Sam turned things on their head, grim faced as they ran. Nightmarish images of corrupted programs, blood everywhere, Quorra staring at him with those dead eyes, Alan shot dead, his apartment in flames.<p>

He wrapped his arms around his waist, hugging himself as he worked through his grief, his utter helplessness; he hadn't been able to do a damn thing to stop everything from crumbling to pieces. He'd lost everything, and now he was in his father's position, trapped in the Grid, and he had to laugh at the irony, the sound too high and hysterical to his own ears.

He cut the desperate sound off, unwilling to hear just how worn down he'd become. He remembered Alan's last words to him _("You survive, you hear me? No matter what happens, I want you to keep going_..."), and with those words bolstering him, Sam rubbed at his eyes, not surprised to find evidence of tears and he ran a hand through his hair, breathing deeply to try and calm his racing heart.

"Come on, Sam, get a hold of yourself," He whispered to himself. "You can't stop now."

He sighed, and then rose from the bed, stumbled slightly as he regained his equilibrium. Wait... how did he end up in the bed? He distinctly remembered Tron taking up his bed, and he'd been on the floor beside it. That meant that Tron was awake, and someone had moved him.

He'd been here for hours now, but he wasn't sure exactly how long it'd been. Sam decided that should be his first order of business. He'd managed a few hours of sleep before the nightmares woke him, so he figured the portal was closed by now, and he was probably stuck here until some random stranger stumbled across the computer in the basement.

Again, the irony was not lost on him, as he remembered his father's disappearance.

Downstairs, it looked like Gemini had been busy while he slept. The space was less empty, with three barricades set in the middle of the room, with a stack of weapons by each barricade, complete with a sniper rifle and a machine gun set up, both pointed at the door. The two barricades closer to the walls had their heavy-hitter weapons pointed towards the windows.

Huh. The place was set up and ready for war.

Behind the barricades and closest to him, a large flat table had been created, with a complete, and very detailed, holographic display of the city lighting the room up in blue, orange and green light. Sam walked over to the display, recognizing it as a type of map, identifying all the sectors.

"You're awake."

Sam nearly jumped out of his skin, banging his knee hard on the side of the display, swearing loudly as he did. He turned towards the voice, recognizing it as Tron's, though he was a bit startled to also recognize it as Alan's voice.

Then his memory caught up with him, and oh yeah, Alan created Tron in the old system, and he remembered that programs from the old system looked like their Users. And yeah, now that he was looking at Tron, without his helmet, he did look like Alan. Same facial features, same hair, although a dark brown rather than the white he was used to, but his eyes were different, colder, and more dangerous. There was also a thick scar running from the corner of his right eye down his jaw, ending just under his chin.

"Tron," he said in greeting, keeping his eyes on the security program, just in case.

"I thank you, Sam Flynn, for saving my life." Tron kept his distance, recognizing Sam's uneasiness, left over from when he'd been Rinzler. "You weren't obligated to do so."

Sam shrugged, dismissing Tron's last statement. "It was the least I could do, I mean; I couldn't just leave you to die. Besides, Alan_1 asked me to help you if I could."

"My User?"

"Yeah, Alan sent me here." He sighed, deciding to just let go of the past, and start afresh. "Look, a lot has happened, and you're as restored as you're going to be, so we might as well work together, without all this... awkwardness. Sound cool?"

Tron tilted his head as Sam spoke, processing his words before nodding. "Yes, that is acceptable. I feel I must apologize for my actions as Rinzler. I put you, and your father, through a great deal of trouble."

Sam waved him off. "It's ok, I understand. If it helps, I forgive you. Come on; tell me what's been happening while I slept. Where's Gemini?"

Tron came to stand beside him at the holomap, pointing to a specific blue bit moving around the arena sectors. "Gemini updated me on your wishes, so I sent him out into the city to gather more information, since I, too, am lacking on the current situation. The City is bound to be split in its opinion, with different factions fighting for dominance. Some will undoubtedly follow in CLU's footsteps, while others will continue to hold out hope for the Users, in this case, you. Some will be neutral, wanting nothing to do with the fighting, while others will try to force sides, hoping for a kind of civil war." He gestured to other parts of the map, pointing out specific sectors. "The yellow sectors are the remnants of CLU's forces, as far as Gemini can tell me. The green are neutral or unexplored sectors, while the few blue sectors support the User-friendly. The sectors in red are corrupted, still damaged from when the portal blew after the Reintegration."

Sam nodded, taking it all in, a little dismayed at the numbers. CLU's influence was still so strong, and currently outnumbered them. He'd have his work cut out for him, in repairing the Grid. "You're in contact with Gemini?"

"Yes, we set up a secure comm. line with a frequency I used in the old system before Flynn brought me here. It should be untraceable, but just in case, we have set up defences, as you can see." He gestured to the barricades behind them, and Sam grinned, pleased with the progress made. "I equipped Gemini with both a lightcycle and a lightjet, should he need to get back here in a hurry."

"Looks like you have everything under control. What about the portal downstairs? Should I assume it's closed by now?" He asked, even though he wasn't looking forward to Tron's answer.

The security program hesitated for only a moment before nodding, confirming the portal's closure. "I persuaded Gemini to let you sleep when the portal closed with no messages from the outside. You needed the rest."

"No messages, huh? How long was I out?"

"About five and a half hours, though according to the logs, you've been in the Grid for approximately eleven hours." Tron had clearly anticipated his next question.

Heaving a sigh, Sam leaned against the holo console, cradling his head in his hands. This was bad, now he had no control on what was happening on the outside. It was out of his hands now.

"That means that something's happened to Alan. Either he was captured and killed, or died of old age before making it safe for us, but it means that he's probably dead, and I'm trapped here, just like my father was." Tears misted his vision, so he shut them, feeling them fall.

There was a hand on his shoulder, grounding him to reality, comforting in its presence, and Sam could very easily comprehend how this program had been his father's friend and companion, and the sobs began to wrack his body, tearing through him. The hand on his shoulder pulled at him, drawing him into a strong embrace, and he sobbed into Tron's chest, clinging to him as his grief raged.

He_ really_ needed this chance to grieve, to let everything out.

Tron just held him, carding one hand through his hair as he purred, the sound vibrating through Sam as the tears slowly subsided until he was just drained emotionally, dragging breath into his lungs.

"...It wasn't supposed to happen this way, you know," Sam's voice was shaky but strong, the words soft. "We were doing good work, making history and just beginning to do everything that Dad predicted with the ISO technology that Quorra had in her DNA. I used Encom to branch out into discovering medical breakthroughs, the beginning of bioengineering, all sorts of technological advancements designed to benefit the human race.

"In just a year and a half, there were already rumours that we were well on the way to curing a whole lot of debilitating diseases, deadly cancers. We'd already improved or invented surgical techniques, already made progress in neuroscience. That's just the stuff we branched into.

"We made dramatic advancements in technology in general, faster computers and better AIs and NASA was after us to help with their space program, to help build better rockets and better ships, and since we partnered with them, they haven't lost another shuttle. Last week, they were talking seriously about a manned mission to Mars, and we were going to help with them with that. We were doing so much good.

"But something happened. I knew the government was after us for military contracts, but I always refused them. There was no way I'd use my father's legacy to create more ways to wage war. It was difficult enough keeping them out of our medical and bioengineering research.

"The entire time, I worked on trying to repair the Grid, using Encom's resources to back me up, learning all of Dad's tricks and just trying to understand what he did. One of my best programmers, I never fully trusted him, seemed too self-serving to fully trust him, he somehow hacked my security, maybe I was too careless, I don't know, but he found my research on the Grid, and the truth of Quorra's ISO origins, and he turned it over to the military.

"They came after us. I was away from the office when they triggered my security alarms digging through Encom's computers, wiping all the files and research. The alarms were sent to the tablet I always carried with me, so when I got the notice, Alan came with me to check it out.

"I found Quorra in the med lab, by one of the computers there, so she must have gotten rid of the research in the lab. There was a hit team in the lab too; standing over her body, so all I could do was run, leaving her there. It was like she was staring at me, with those dead, lifeless eyes, and I ran. I managed to get Alan on the way down, the hit team behind us all the way, but we trapped them inside the building after we got out. I programmed all the doors to seal shut after we got out.

"We ran, first to my apartment, but it had been destroyed long before the move on Encom, the fire was already dying down. We couldn't go to Alan's, or to any of our friends', so we just ran into the streets, dodging the military for as long as we could.

"We ended up at the arcade, where Alan came up with this crazy idea to send me here, so I finished uploading the upgrades to the Grid and he made sure they wouldn't find the computer or the laser, and he told me to change the world, and to take care of you."

Even though he had only just woken up, Sam was so tired, he just wanted to sleep. Oddly, he was relieved, having finally told someone, having shared his grief. He didn't even mind that it was Tron he took comfort in. The program felt safe, and was reassuring now that he wasn't controlled by CLU and his Rinzler aspects.

"You did everything you could, Sam. None of it was your fault, and I grieve with you." Tron still ran his gloved fingers through Sam's hair, calming him, and the program felt a sense a peace he hadn't felt since regaining control in the Sea of Simulation, or during any of his encounters with Flynn before CLU had destroyed everything.

Sam blinked away the remaining tears, and reluctantly removed himself from Tron's safe embrace, grateful that the security program hadn't pushed him away. But they really did have a lot to do still, so he couldn't just drown himself in despair, no matter how tempting it was at the moment.

"Thanks for that," He shrugged again, embarrassed. "But I'm sure we've got plenty to do still on the agenda."

Tron recognized the need to keep busy, so he just nodded and brought Sam's attention back to the map, pointing to the corrupted sectors; there were about thirty of them. "These sectors are the most dangerous, because not only are they currently impassable, they're also a perfect nesting ground for gridbugs. The bugs cause enough problems coming from the outlands, so your first order of business should be to repair these sectors."

"Gridbugs?"

"Yes, they like to feed on programs and stray energy, causing deresolution in their wake."

Sam wrinkled his nose in disgust. "Why is it always bugs?"

Tron just smirked at him, and together, they were able to devise the safest way to the closest corrupted sector, and other sectors, bypassing potentially hostile programs, and as soon as Gemini returned, the two of them would head out to the streets, to manually repair the sector, with Tron as his back up. They'd be taking lightcycles there, and Sam managed to convince Tron to equip himself with a shield, just in the off chance they were attacked. Sam would have his weapons, the light swords and blasters, along with his disc, but he just wasn't as skilled at fighting like Tron was.

With luck, they would be able to repair the corrupted sectors with little to no interruption, and hopefully avoid the hostiles altogether.

* * *

><p>Another explosion erupted behind him as he raced away on his cycle, swerving around the debris, and all Sam wanted to do was stop and go kick some ass! But damnit, there were too many of them on his tail, and Tron was right beside him, racing through the streets, leading them away from the safety of the arcade. Sam couldn't really fault Tron for this, since they were far too outnumbered, and their only chance lay in outrunning their pursuers.<p>

He was having an odd sense of déjà vu, and it was pissing him off.

Things had been going so well, too! He had time to reflect on events as he followed after the security program just ahead of him. He and Tron had gone out to the first corrupted sector and repaired it, a quick in-and-out job, gone from the sector before anyone knew they had even been there.

Gemini had stayed behind, keeping an eye on the arcade and protecting their home base while they'd been gone. He would continue to do so every time Sam and Tron left for the streets to repair the other sectors, and Sam was grateful for that, knowing that his creation had everything under control.

Their second trip out had also been a success, though it was clear that word was starting to spread already, as there had been more programs in the area, forcing them to be more cautious. The gridbugs caused some issues initially, trying to chew on Sam as he uploaded the repairs, but Tron had been there to take care of that particular problem.

Once they'd returned from the second sector, Gemini went out again at Sam's command, to sound out some of the User-friendly sectors, with the hopes of bringing back a few programs to help them with defending the arcade. The sector the arcade was situated in was getting more and more traffic, and it was starting to make Sam a bit paranoid.

Gemini had been successful, bringing back three programs, armed to the teeth, and showing all the signs of battle and war. They had consented to submitting to mild repurposing by Sam, although all he did was ensure that they would not be capable of attacking either himself, Gemini or Tron, nor would they be able to inform other programs of their location. He'd left their other functions untouched.

The third sector had been more difficult, as the gridbugs were particularly vicious, but there had been no interference from the surrounding sectors. By the time Sam and Tron had returned to the arcade, he'd been trapped inside the Grid for about twenty seven hours, or fifty five years, give or take a few months.

He tried not to think about that.

Shortly after their return from the third sector, the arcade had come under attack. A faction of CLU's followers, most likely noticing the increasing traffic in this sector, had decided to attack, for some reason that Sam couldn't fathom. The battle itself was now a blur, a steady rush of adrenaline, laser fire, and derezzed code shattering from the force of Tron's dual disks.

Once the adrenaline wore off, Sam had been exhausted, so he took the opportunity to get some more sleep while he could; leaving the task of cleaning up after the brief battle to Tron and the ever-efficient Gemini, knowing everything was safe in their hands.

He learned from Tron that Gemini left for the central sectors to spread rumours of his return and his efforts in restoring the Grid, spreading word of the repaired sectors, hoping to incite riots against CLU's remnants. It was still too early to really tell, but there were already hints that it was working.

At thirty seven hours inside the Grid (seventy six years), there was another attack on the arcade, but it didn't last long, as Sam had been able to test out the grenades he created after he'd woken up.

Sam and Tron had gone out again, for their fourth corrupted sector, determined to restore as much as he could and while the actual repair work had gone off without a hitch, they'd been ambushed as they left, and bringing them to the high speed chase they were presently engaged in.

Sam revved his cycle, bringing him right next to Tron. "Hey, we really need to lose these guys!"

Tron glanced his way, keeping most of his attention on the road in front of them. "We should split up, think of it like the Games!"

"Divide and conquer, I gotcha!"

They veered away from each other, Sam going left down a side street and Tron doing the same on the right, with the hostiles behind splitting up to follow both of them. As Sam sped through, he reached down and grabbed one of the swords he kept attached to his hip, igniting the blade and keeping it close to his side, feeling the heat of the laser even through his suit. Once he had enough room, he spun his cycle into a sharp u-turn, the bike almost parallel to the street, before speeding towards his pursuers, blade held out away from him, ready to strike.

He attacked the hostile programs chasing him fast and hard, slashing through several of them before they even knew what hit them. He ducked down another side alley, drawing the rest of them deeper into the maze.

He jolted forward as one of them rammed his back bumper, trying to make him lose control of his cycle and crash. He smirked, they really underestimated him. On the back of a bike, no matter what variation, he was virtually unstoppable!

He was rammed again, but this time, Sam countered by swinging his blade in a back downward slash, and the sound of derezz met his ears. He revved forward, speeding away, turning sharp corners in his efforts to keep ahead of the enemy behind him.

He raced into the next sector, this one was User-friendly according the map he'd memorized, and the first open space he came across, Sam leapt from his cycle, deactivating it. He rolled to his feet smoothly, drawing his disc with his free hand, ready for a face off.

As the first pursuing lightcycle came into view, Sam threw his disc, watching it arc beautifully, cutting down the enemy program. He got another as they passed him with his sword, deflecting a disc strike with his shield in the same move.

There were only three of them now, and they were intent on killing him. They circled around, coming at him from different angles, and Sam knew that he only had one chance to not get killed.

He threw his disc as they closed in, hitting his target dead center, and he followed the momentum of his throw to bring his shield up, blocking the disc strike from the second target while cutting down the third with his blade. He kept moving, spinning tightly to bring his blade up, slicing through the back end of the lightcycle before it past him completely, and sending its driver flying.

For a moment, he stood there, his breathing heavier from the exertion from that awesome move he managed to pull out of his ass and he succeeded into pulling it off! Elation bubbled in his chest, and a grin tugged at his lips as stunned laughter echoed in the sudden quiet.

"Wow, I can't believe I just pulled that off." Sam shook his head, still grinning. "I should find Tron."

He had to search for a bit before finding his lightcycle baton, but then he was speeding away, backtracking through the sector's alleys to where he and Tron had split up to ditch their pursuers.

He wasn't really surprised to find the security program waiting for him, propped up against a wall in the shadows of a towering skyscraper, and he slowed his cycle down only long enough for the other to recognize him before speeding away for the arcade. It was only a few moments before Tron was at his side, racing with him and Sam had to grin under his helmet.

It was a sign that Tron was beginning to heal.

At least he was doing something right.

* * *

><p>77 hours later, Sam was more than ready to collapse where he stood and just sleep for a week, at least, and ignore everything that was happening around him. The past three days had been hell, and while he was grateful for the distraction the chaos provided, Sam was exhausted and about near his limit.<p>

In the 77 hours that has passed since he and Tron had returned from their fourth restored sector, he had created more programs, security drones under Tron's command, the arcade had been attacked on three separate occasions, he'd managed to repair another eighteen sectors, he'd been attacked in those sectors at least five times, and at the end of five days since arriving in the Grid, he maybe slept for about twenty four hours total. The last sixteen hours, he and the rest of his meagre posse of allies have been engaged in full-out war. They were currently hunkered down in the arcade, possibly looking at a ceasefire.

He was exhausted. No, he was _beyond_ exhausted. For the moment, there was a brief respite in the fighting, so he quickly finished his task of creating more defences and weapons, like the reinforced walls, and the energy grenades that were ridiculously efficient in offlining the programs attacking them, the remnants of CLU's repurposed forces.

Standing slowly, he sought out Tron, finding the security program at the map display again, processing the data there. Tron had come a long way during the last few days, almost clinging to Sam for the familiarity Sam gave him, reminding the program of his time with his father. He wanted Tron to trust him, to treat him like he had his father, and well, to be his friend. It was so easy to see beyond the bad experiences of Rinzler and see the gentle but strong program Kevin Flynn had told him about in his childhood stories.

There was also Alan's promise, so he was doing what he could to heal the program, being his friend, being the source of redemption that Tron felt he needed. Sam had already forgiven Tron, because it had been CLU's repurposing that had almost destroyed Tron in the first place, and the program had more than made up for it in Sam's eyes.

He came up beside the security program, so close he could feel the heat of the body next to him. "So, how do we stand?"

Tron pulled his gaze away from the holomap, his manner softening as he acknowledged Sam. "Currently, we have a ceasefire. We're barely maintaining our defences, and we have you to thank for that, but they are experiencing enough casualties to their numbers to make them pause in their assault."

"So if we don't find a solution soon, we're boned."

Tron looked around, noting the close proximity of the SecDrones and the few allies they'd recruited from other sectors. He tilted his head, motioning for Sam to follow him as he led the User to Sam's room upstairs, away from prying eyes and ears. Once they were hidden away in the privacy of the back room, Sam lay in a boneless heap on the bed, with Tron sitting down next to him.

"I worry about you, Sam. You're doing too much. I wish there was more I could do."

Sam shrugged, eyes closed as his exhaustion once again made itself known, settling in his limbs like lead weights. "Not much we can do about that, not with them wanting to kill me. You know, being a User sucks balls right now!"

Tron laughed lightly at him, a small smile lighting up his whole manner, and Sam couldn't stop his own grin, not that he wanted to.

Before anything else could be said, there was a knock at the doorway, alerting them to Gemini's presence. The highly adaptive program had an air about him that Sam picked up on immediately, an excited energy that piqued his curiosity.

Tron sensed it too, frowning at Sam's aide. "What is it, Gemini?"

The program grinned widely, dark eyes glittering with near-manic excitement. Sam pulled himself into a sitting position, giving his creation his full attention and wishing he would just tell them already.

"There's a message!"

"What?"

"Are you sure?"

Both he and Tron spoke simultaneously, and Gemini's grin widened further. "Of course, I'm sure! I check the portal every six hours when I'm here, and there's a message."

Sam couldn't do anything for a minute, his mind processing the words leaving Gemini's mouth. He rose from his bed, brushing past his program with one goal in mind; getting to that console downstairs to see that message for himself.

There was a message.

He heard Tron say something, but he wasn't paying attention at all, as he hurried down to the portal room, and yeah, there was an open chat window on the terminal screen.

_/Hello?/ _

* * *

><p>AN: I TRIED TO DO THE BEST I COULD FOR INSIDE THE GRID, WITH THE APROPRIATE LINGO, BUT IF THERE ARE ANY GLARING ERRORS, DON'T HESITATE TO INFORM ME OF THEM.


	4. Chapter 4

TRON: New Frontiers

* * *

><p>CHAPTER 4<p>

* * *

><p>It was the perfect day to be outside, instead of being stuck in a stuffy office with his paperwork, no matter how nice an office it was, so Christopher Pike, Admiral and Commandant of Cadets, was immensely pleased with himself for taking control of this simple project, away from Starfleet HQ in San Francisco, and away from those interfering and nosy doctors at Starfleet Medical.<p>

He was up and walking, although with the aid of crutches, because Leonard McCoy was a medical genius and it's been a year since what was now dubbed the Narada Incident, so he was fine, thank you very much.

So when the opportunity arose to scout out a potential recruitment office in Central City, he jumped on it like a dog with a fresh bone. He was still the best recruitment officer in the 'Fleet, damn it!

At the moment, he was standing across the street of the potential site, an empty shell of a building in an old industrial sector. The building itself was partially collapsed, with only one wall towards the back remaining intact, a relic from the late 20th century.

It would be easy enough to demolish the rest of the building and build the recruitment office from scratch; he wasn't too concerned on that. It was a very good site, and the industrial sector was slowly being transformed into an active urban community, drawing people into the area. Pike didn't think there'd be any real problems.

"Admiral!" A young lieutenant came running from the building, a datapad in hand. He didn't look overly concerned, but rather kind of excited.

"Yes, Lt. Williams?"

"We found something I think you should see, sir."

Pike was curious now. "Really? What kind of 'something'?"

"There's a secret door that according to scans, lead to a basement not in the original floor plans."

"Really now? Well, lead the way, lieutenant."

The building, an old fashioned gaming arcade from the late 20th century, had already been gutted, emptied of all the debris accumulated from the past 200 years, except for an ancient, decrepit machine on the intact wall. Pike recognized the machine as an ancient gaming console, almost unrecognizable from wear, tear and grime, but he was just able to discern the name at the top of the machine.

Tron, interesting name for a game.

"So, where's this secret door?"

The lieutenant gestured to the old console. "Behind there, sir."

Upon closer examination, Pike was able to see the worn gouges on the cement floor, revealing that the machine swung outward, but more disturbing was the signs of projectile weapons fire. He ran his fingers over the old holes riddling the console and the wall, eyeing the suspicious rust coloured stains near the floor.

"This place was attacked; probably the same time the building collapsed, preserving the little evidence there is left. Were there any other signs of this?" Pike asked, indicating the holes in the wall and in the game console.

"Just by the entrance, sir. The damage looks old, so we didn't think much of it."

Pike nodded. "It is old, at least 200 years. I think whatever happened here, the answers are behind this door. Open it up." He moved out of the way, giving enough space for his men to work. It took three men to move the rusted machine, revealing a solid steel door that turned out to be sealed shut from the inside. There were also more rusty stains and bullet holes denting the metal.

"I want this door cut open immediately, and oxygen masks. We're looking at a tomb here, unopened for the past 200 years."

It took no time at all for the door to be cut open and removed, revealing a pitch black, partially collapsed, musty smelling stairway leading down. Pike, followed by two security officers, manoeuvred his way down the fairly steep stairs, hanging fluorescent glowsticks every few meters as he did.

The basement was situated directly beneath the main floor of the building upstairs, with two rooms, as far as Pike could determine. He wasn't terribly surprised to see the skeleton next to the door leading to the other room. Most of the clothes had rotted away over time, leaving only scraps behind, but there were some visible bits of plastic, a rusted weapon at its feet, and a pair of dusty glasses

This person had died protecting something, of that Pike was certain. That something was behind the locked door, and he wanted to know what it was.

After the security guys broke the decrepit lock and opened the ancient wooden door, Pike entered the second, smaller room, preparing himself for anything he might find.

He didn't expect a functioning computer. The terminal was fairly massive, about the size of his office desk, but it was surprisingly advanced for its age, with glowing touch screens that Pike knew better than to touch, and as far as he could tell, the system was completely independent, running on its own power.

There was another machine in the room, its purpose Pike couldn't determine. He decided not to investigate.

He was out of his depth here, Pike knew that. This technology was old, but advanced. He knew he would need someone with an extensive knowledge in ancient tech, but with a considerable amount of experience in programming.

Shit. There was only one person he knew of with both of these qualifications, and it helped that the kid was a genius, too.

He needed Kirk.

* * *

><p>James Tiberius Kirk was excited to be back on Earth, happy for the chance to give his crew shore leave to spend time with family before they shipped out to the Neutral Zone again.<p>

He was also very curious as to why they'd been recalled, why he, specifically, had been requested by Pike. He didn't have all the details, but Pike had found something that needed his specific skill set, though he would be bringing both Spock and Chekov with him, since he was sure it was engineering, computer software or hacker related, so he was, of course, going to bring with him the smartest people he knew.

He and his command crew were currently on the last shuttle coming down from the Enterprise, and as he stepped off the shuttle with Spock at his side, and Bones grumbling away behind him, he wasn't surprised to see Pike waiting for him, the Admiral leaning slightly on a cane, though he could see a pair of crutches in the arms of a lieutenant behind him.

"Admiral Pike, always a pleasure to see you, sir." He greeted with an easy salute and his customary cocky grin.

"At ease, Captain," Pike smirked at him, unfazed like always with his usual antics. "Come on, I'll explain on the way."

Straight down to business, then. Ok, he could work with that. He motioned for Bones and Chekov to join him and Spock as Pike switched to his crutches before leading them out of the hanger to a smaller commercial shuttle waiting for them.

Pike waited until everyone was seated and they were in the air before handing out PADDs for each of them. Jim browsed through the contents briefly, wondering briefly at the floor plans of a building he didn't recognize and some fascinating schematics for a machine he would love to try and build.

"What you're looking at is the site of the recruitment office Starfleet will be building in Central City. The reason I've asked for you, Kirk, is because we found something, a computer, in a hidden basement beneath the main floor."

"And none of the techs planetside can do anything with it?"

Pike shook his head. "I don't want them even touching it. The computer's old, very old, but it's running completely on its own power. That basement's been sealed since before the Eugenics Wars. There were also multiple signs of combat, projectile weapons fire, to be specific. The computer, and the other unidentified machine in that basement, was the target of an attack on the building, and someone died protecting it. I want you to find out what was so important about that computer."

"If the technology in question is so old," Spock said. "Why should we investigate at all? Would it not be more efficient to simply dispose of it? The information within would undoubtedly be obsolete."

Pike grinned at him, reminding Jim of an excited child. Not that he'd admit that aloud. "Just a feeling, Spock. This is important, more than we can know."

McCoy graced them with an eye roll. "Besides, hobgoblin, anything pre-WWIII is valuable since we lost so much of our history in those wars, specifically of those years."

Ok, that made sense to Jim, and knowledge was power, as the saying went. He also trusted in Pike's 'feelings', hell, he was a good example of Pike's crazy intuition! He still had one question, though. "So, why me? I mean, specifically."

There was a particularly smug look on Pike's face as he turned that little smirk of his on Jim, a glint in his eyes that made him a little nervous, like all his secrets were about to be revealed. "I wanted you, Kirk, because you're a nerd."

Spock's left eyebrow shot up to his perfect hairline as McCoy tried, and failed, to contain his startled laughter as Jim sputtered indignantly. Chekov just watched, a little stunned.

Pike's grin got that much wider. "You're one of the biggest history nerds I know, of all things old, like the paper books I know you have squirreled away somewhere, and your collection of ink fountain pens that you restored so you could actually use them. You'll be careful with tech this old, and since you're arguably the best hacker in the 'Fleet, you should be more than capable of cracking the system without damaging it."

Jim felt like pouting, but he was a Captain now, so he had to act all captain-y. "How do you know about the pens?"

Pike only shook his head, still grinning. "Sorry, kid, I can't give away my secrets. Anyway, Spock, Chekov, I would like both of you to work on the other piece of equipment we found. I want to know what it is, what it does, what it could possibly be doing down in that basement. As far as I could tell, there's some minor damage, probably from the ridiculous amount of dust in that room, so all I want you to do is restore it. Don't go messing with it unnecessarily until we know what it is.

"McCoy, we found a body down there, too. Whoever he was, he died protecting that room, sealing the basement from the inside and effectively making it his tomb. I want you to find out how he died, and if possible, who he was. He deserves a grave, at the very least." The doctor didn't give a verbal confirmation; rather he started digging into his ever-present medical bag, undoubtedly checking his equipment.

"What about the history of the building itself? What was it used for prior to its collapse?" Pike was right, he was a nerd, but damn it, he was curious about a lot of things.

"We found out, from what records we could recover, that it was abandoned in the late 1980s, after its owner, Kevin Flynn, went missing. It was a video game arcade in that decade, run by the owner, and Flynn was also CEO of Encom, the main programming and Software Company of the time. Flynn was seen as a programming genius," Pike looked at each of them, aware that he had several certified geniuses right there with him. "Pioneering most of the advancements of the era by leaps and bounds, while also creating some of the most successful games in the early history of gaming. He also revolutionized computer and software development during his time as CEO before he disappeared without a trace in 1989. Under suspicious circumstances that I don't have the details of, his son disappeared in much the same manner twenty two years later, only a few years before the start of the Eugenics Wars."

The shuttle touched down on solid ground, meaning they had reached their destination, and as they filed out of the shuttle, Jim was able to take in his first impression of their objective. Pike was right, the building had, once upon a time, come under an attack of some sort. The surrounding architecture was in remarkably good condition in comparison to the almost complete destruction of the future recruitment office. The damage seemed... almost controlled, like it was engineered to collapse inwards, obliterating the building with minimal damage elsewhere. Any physical evidence of the controlled explosion had long ago been lost to time, and as he walked through the empty shell of the building, he picked up the signs of weapons fire as mentioned by Pike, both at what remained of the front entrance and on the intact back wall. He noticed that most of the damage, while obliterating the main floor, hadn't damaged the foundation, hiding the entrance to the basement, partially collapsing the stairs and protecting the hidden rooms below.

He wondered how Pike had managed the stairs, or what was left of the stairs, with his crutches.

Jim was relieved to see that Pike's team had the basement well lit, and cleared of rubble, giving him and his crew suitable space to work. Bones went to work right away on the skeleton, pulling out his tricorder, looking for things that he didn't really care to understand. Bones was the doctor, not him; he didn't need to understand the medical stuff.

While Spock and Chekov went to work examining the other machine, Jim turned his focus on his task, realising what Pike meant about the ancient computer. It was an interesting design, very sleek and modern, despite its age, and yes, it was up and running, a very quiet humming sound that was surprising for what he knew of the era's technology. He peered around to the back of the machine, noting the cable plugged into the wall, but he knew that a building this old and in this state of disrepair hadn't been attached to any power grid for many, many decades, so how was the computer functional?

A scan with his own tricorder revealed that the computer was creating more than enough electricity to power one of the Academy dorms, probably, and that something, some function of the computer itself, was converting the electrical power back onto itself. He couldn't fathom how that was possible, but it proved that the creator of this system was ridiculously creative and ingenious.

He wiped away the dirt and dust accumulated over the past 200 years from the main screen, bringing it out of hibernation, and with a few key strokes of the digital touchscreen keyboard, he was able to bring up the main operating system, noting that two programs were running, something with the label The Grid, and an activation screen of some kind, but he decided to leave that alone for the time being. He really didn't want to mess with anything he couldn't safely identify.

Jim sighed, rubbing at his eyes. He could tell this was going to be challenging, simply because of how old this operating system was, though it was surprisingly fast and easy to navigate, well, for him, anyway. He brought up the files on the Grid, frowning at the code that appeared on the screen, looking very much like a map at first glance. The system had been largely corrupted at one point, but most of the damage had been repaired throughout the years, though he couldn't identify who, or what, had done the repairs.

The Grid was very active. That much was clear as he investigated, browsing through the code, and he wondered if there was some way he could communicate with the system, so he hunted around the portal, and there! A message board to the Grid, which was weird, because that made it seem like there was intelligent, sentient life of some kind on the other side of the board.

Well, he might as well give it a shot. It was that or to start digging through things he wasn't sure he wanted to, like that other program currently running. So he pulled up the message board, looking very much like an old fashioned chat room, and typed in a very simple message.

/Hello?/

He didn't expect a reply right away, hell, he wasn't really expecting anything at all, so it was a bit of a shock when the computer beeped, a chime like sound, alerting him of a reply.

_/Hello. Who are you?/_

The response seemed fairly human, like he was speaking to a person, and it made him very curious.

/Name's Jim Kirk. You appear to be sentient. Are you the computer?/

_/No, I'm a User, I'm just living inside the computer, in the Grid./_

Huh. That was interesting, but how was that possible? What, then, was the Grid?

/The Grid?/

_/It's the name of the system, the computer hardware just houses it. Can you tell me if there's a laser behind you? I'm assuming you've moved nothing yet./_

A laser? That's what it was? Jim turned to look behind him, where Spock and Chekov were still working away on the machine, tools in hand. "Hey, have you guys figured out what you're working on?"

Spock looked up from his tricorder, regarding him blankly, but he could tell from the slight furrow in his brow that the Vulcan was slightly frustrated. "I believe it is a primitive laser of some unknown fashion, but neither myself nor Lt. Chekov have come to the conclusion of its purpose."

Kirk grinned at him. "You're right, it is a laser. I can find out what it's for, if you'd like."

Spock refused to answer him, but Chekov nodded, excited. "Please, Keptin, that vould be most helpful."

"Sure thing, Chekov, coming right up."

/Yeah, there is. It's a bit damaged, but we're fixing it up now. What does it do?/

_/It's my only chance to leave the Grid. It digitalizes atoms and reintegrates the atoms inside the Grid, like transporting something, or someone, from the outside where you are, to the Grid, inside the computer./_

Kirk was stunned, this was amazing! This kind of technology didn't currently exist, yet it was a couple hundred years old! The potential for this was astounding, and the possibilities raced through his mind, incomplete ideas just waiting to be explored.

He turned back to the laser, where Spock was watching him. "You'll never believe this; that laser lets you go inside the computer. It digitalizes matter, working much the same way a transporter pad does, just you know, a bit different."

"And may I ask how you acquired this information, captain?"

"I never did ask his name, gimme a sec."

/The laser is fine, got my best people on it. By the way, I never did get your name./

_/My name is Sam Flynn./_

No way. This was too much of a coincidence. /Any relation to a Kevin Flynn?/

_/He's my dad./_

"Holy shit."

"Is there something wrong, captain?"

"Get Pike down here, he needs to see this." Kirk barely heard, barely paid any attention as Spock left the room, his attention focused solely on the screen in front of him.

/We knew Flynn had disappeared, and you vanished too, but your name was never mentioned in the reports./

_/Oh, that's... interesting. I have a question for you; who are you really? You said 'we', meaning you're part of something, an organization of some kind, and you also said 'my people', meaning you have authority./_

Jim hadn't been expecting that. Sam was smarter than he'd realized. He figured it couldn't hurt to tell him the basics at least, since Sam was going to be associated with Starfleet for the next while.

/You're right, I'm Captain James T. Kirk, of the U.S.S. Enterprise, a starship. We're explorers, scientists and diplomats for the most part, but sometimes we're soldiers./

_/You're military? What would you do with this technology?/_

/That's not up to me, but I don't think the Admiralty would do anything wrong, not with Pike as an Admiral. He's someone I trust with my life, and he's never let me down. Why are you so worried about the military?/

"Kirk, what'd you find?" He jumped at Pike's voice behind him, and he scooted his chair over, giving the admiral a view of the screen.

"Kevin Flynn's son has been living inside the computer for over two hundred years. Sam told me about the laser, which is super cool, and he's also worried about military involvement."

"You told him who you were?"

Kirk shrugged, not too concerned. "He'd already figured it out. I figured it wouldn't hurt to share some details since he'll probably be working with Starfleet once he's out."

Pike nodded, satisfied with his reasoning. "Ok, let him know we're peaceful, and find out why he went inside there in the first place. I have the feeling we barely know anything of the real story."

"Can do, sir." He looked back to the message screen to find Sam's answer waiting for him.

_/The military, backed by the government, is why I had to hide here in the first place. They hunted us down./_

That was a very good reason to be wary of any kind of military. /I got good news for you, then. Starfleet is more based in the sciences than any military applications, more like a humanitarian armada. We do learn defence and tactics and stuff, but that's because not all life in the galaxy is friendly. How come you're in there?/

_/Are you safe I'm safe?/_

/I promise. I will do everything in my power to make sure you're safe./

_/Ok. To start with, you need some history, a bit of back story. In the early 1980's, my father, Kevin Flynn, dreamt of a world he thought he would never see, a world inside a computer. Would the circuits be like freeways? What would it look like? One day, he got in. He created the Grid, and the programs were people, living beings just like us, and with the help of a program he brought over from an older system, and another he created himself, he created a world here, inside the Grid./_

Kirk could barely believe it, this was amazing! Flynn was certainly a genius, and it looked like his son was one, too. He kept reading the text as it appeared, knowing Pike was doing the same over his shoulder.

_/There was an uprising. CLU, Flynn's program, came to believe that Users were obstructing the way for a perfect system. My dad wasn't able to get to the portal in time, and he was trapped in here. He was trapped for twenty years, but to him, it was more like a thousand. He found something special, a miracle that would change everything we knew about everything. Disease would be gone, religion would change, philosophy, science, everything. The uprising almost destroyed the miracle, although one survived. When I came down here the first time, I found my father, we fought off CLU and we were able to bring Quorra, the last remaining ISO, the last chance for a miracle, to the world outside. My father didn't make it./_

/So what happened?/

_/We started using the ISO technology in medicine, bioengineering, technological developments, physics, all sorts of things. We were doing so much good. We were changing the world, just like dad dreamed of. The problem was that the American government wanted to use the ISO tech for military purposes. To make better soldiers, better ways for humans to kill each other. I kept refusing until they came after us. They killed Quorra, and I only escaped with luck, along with Alan Bradley, dad's partner and my mentor. It was his idea to send me back here, although I was able to reverse the time flux, so from my perspective, I've only been down here for approximately 121 hours, or five days. If my calculations are right, the year should be 2259 or 2260, at the latest./_

Kirk stared at Pike in alarm. Five days? If his math was correct, and it usually was, that meant every hour spent in the Grid was the equivalent of two and half years on the outside. That was insane! "What do you make of this, sir?"

Pike wore a deep frown and sighed. "That kid is very brave. He knows how much time has passed."

/Ouch, that really sucks. That's a long time./

_/I know. I'm coming to terms with it./_

/I'm sorry about your friend, the one who was killed. So this Alan is down here with you?/

_/No, he sent me down here alone. He said he would make sure they would never find me until it was safe. I started worrying five hours in, but I knew he was dead after ten hours with no word./_

"Do you think the body in the other room could be Bradley?"

"It's looking like it. I'll get McCoy's report." Pike hobbled his way out, and only a few moments later, he returned with Bones, who was looking grim.

"What do you got, Bones?"

"The victim, identified as an Alan Bradley, died from several wounds caused by an old fashioned projectile weapon called a gun, to his abdomen and chest area. After he got shot, he probably only had time to get down here before he died. He was carrying what has been identified as a detonator, leading me to believe he caused the explosion that collapsed the building. He was close to both Flynn and his son. The reports are kinda sketchy, like anything from that era." He shrugged, dissatisfied that he couldn't find more information.

"If it helps, he saved Sam Flynn's life. I'm talking to him right now."

"What? How?"

Pike grinned at him. "Don't worry doctor; I'll fill you in."

Kirk grinned at his best friend, knowing this would take some time for the doctor to get used to. The computer console beeped again, so he turned back to read Sam's new message.

_/Do you have any experience in programming?/_

Kirk had to laugh, ignoring the others in the room, but he couldn't blame Sam. /Yeah, I'm the best hacker in the quadrant. What do you need me to do?/

_/I need you to fix the time flux, bring it back to a reasonable level, because right now, every second in here is five hours where you are. I think the Grid is currently compensating for the time difference while we talk, though./_

Huh, that was interesting. It did explain why Sam had only spent almost a week in the system. /Sure, want to walk me through it, to save some time?/

Apparently Sam thought this was a good idea too, so for the next hour or so, Kirk followed Sam's instructions in surfing the code, hacking his way through, and wow, he was impressed. Seems like Kevin Flynn wasn't the only programming genius in the family. Sam's modifications were fairly elegant, smooth, clean and efficient, much like Spock's programming, but oh so different and sleek. He was kind of jealous, actually.

Sam would prove to be a challenge, if they were ever to face off.

When he was finished, the time difference were a lot closer, and better for them. An hour inside the Grid would only be a half hour out here. He closed the windows he'd opened to change the difference and relayed his success to Sam.

_/Excellent, now I don't have to worry so much./_

/Hey, I have a question. You mentioned that you were hunted down because of ISO technology. What does 'ISO' mean?/

_/The ISOs were different. They had no User, they were not created by any being outside the Grid. The ISOs were naturally occurring programs, and according to Tron, the circumstances of their spontaneous creation have not been seen since that first time. ISO stands for Isomorphic Algorithms./_

Now, Kirk knew his history. He loved history, and all forms of it, from artefacts to events. He knew exactly what historians thought was the cause for the Eugenics Wars almost 250 years ago, and he really didn't want to tell Sam what he knew.

But he knew he had to. He liked Sam, even without really meeting the guy, and Sam deserved to know the truth.

/Um, I hate to break this to you, but you do need to know. We don't know for sure, since a lot of records were lost, but its theorized that Isomorphic Algorithms were what prompted Eugenics research, leading to the Eugenics Wars and World War 3 following that. I am so sorry./

_/What?/_

Damn, he wasn't taking it well. /I'm sorry./

_/When did these wars happen?/_

/The Eugenics Wars began about five to ten years after you vanished, I think. Again, I don't know for sure, with the lack of accurate information available./

_/They must have kept her body, used her DNA. They corrupted everything we were trying to do! We were curing disease!/_

Pike came up behind him, quickly reading through the text. He sighed, shoulders slumping ever so slightly. "Damn, that really sucks for the kid. Tell him he's safe from that, we don't want a repeat of the wars. We're also packing it up, laser's been repaired and we're heading back to HQ. I want to speak with the kid in person."

/We won't let that happen again. We don't want another war. This time, we learned from our mistakes, and the only eugenics research we still use is to save lives, like surgeries, prosthetics, regeneration to some degree./

_/Ok. Thank you./_

/I've just been told that we're packing up here, and we'll be moving both the computer and the laser to Starfleet HQ, probably to one of the engineering labs, so that we can get you out. Admiral Pike would like to speak with you in person./

_/Let me know when you get there, and I'll talk you through hooking up the laser to the Grid. I have to tell you, the portal can't be opened from the inside, and it won't open from the outside without someone coming down here. Once it's opened, I can get out, bringing whoever comes in with me./_

That was good to know. /Cool. Digitalization is safe, I assume?/

_/Oh yeah, you can't even die of old age. The only dangers are getting hit with a virus, literally, and death by derezz./_

That was a new one. /Derezz?/

_/Sorry, I meant deresolution. I don't know how it affects humans, but programs will shatter in a remarkable display of pixels when derezzed./_

Huh, interesting. Maybe he should convince McCoy to go inside once they got set up. /Ok, then I'll probably send in my CMO to make sure you're ok. I just have to convince him first. What's it like when you're hit with the laser?/

_/You don't even feel it. It's almost instantaneous, less than a blink. Your doctor should be fine./_

/Try telling him that. Anyway, I have to go, but I'll speak to you again in a few hours./

He signed off from the chat room, closing all the unnecessary programs and windows, until the screen was blank. He stood from his chair, just as Pike came back into the room, manoeuvring on his crutches with a grace that he was jealous of, since he was under no illusion that he would be as graceful if their positions were reversed.

"Ready to go?"

Kirk nodded. "Yes, sir. How are we moving the equipment? Transporters?"

Pike nodded, motioning for him to follow as they left the basement. Kirk noticed that the body had been removed, probably relocated to Starfleet Medical. He'd have to ask, since he figured that Sam would want to see the remains of the man, since Bradley meant so much to him.

"Yes, I've secured and cleared one of the engineering labs by your old dorm hall, big building by the astrophysics labs."

"I'm familiar with the lab," He grinned at the memories. "Fun times..."

The 'I'm so not impressed' vibe came through loud and clear in the look Pike levelled in his direction, but Kirk was unfazed by it. This was the usual byplay between them, if it didn't happen, something was wrong.

"For that, Sam is your responsibility. I'll get the rest of the Admiralty to keep him with you, and I want him working with us of his own free will." He spoke briefly to a waiting officer, giving the go ahead to transport the computer and laser to the lab. "I have no illusion that he actually trusts us to keep our word to not use his knowledge for more... unethical purposes, so I want you to get him to open up, to trust us. He's going to be cautious, and he has good reason for it, too."

Kirk nodded, understanding completely. "I understand, sir. I'll get the crew to help, after they come back from shore leave. Can you get him on the Enterprise?"

"We'll see about that. I'll have to talk to the kid first before I bring that up before the rest of the admiralty."

He was actually getting excited with this amazing discovery. Sam sounded like a cool, intelligent guy, and the world he lived in was beyond anything he could have dreamed of, and he actually wanted to take a trip down there. Kirk couldn't wait to meet him.

They flew back to Starfleet HQ in the shuttle, and while the techs, under Spock's supervision, set up the equipment in the manner it was found, Pike disappeared to do whatever it was he did, leaving Kirk, Bones and Chekov to head off the mess hall for a chance of dinner. Kirk was going to take this time to try and convince Bones to go into the Grid.

They settled in a quiet corner of the large room with their food, Chekov chattering away about the laser, and the rather complex components that created the machine, and he was excited at possibly seeing the machine in action.

Kirk let him babble for a while, then while the young whizkid stopped to breathe and eat, he turned his attention to Bones. "What did you do with the body?"

Bones barely looked up from his own food. "I had it transported to Medical, I'm going to have the techs there clean it up for a funeral. The kid in the computer's coming out, right?"

"Eventually, yeah. I get the feeling Sam will want to see the remains. Speaking of Sam, I was sort of thinking that you could go inside and check him out."

Bones choked on his food as he processed what Kirk said. "What? What do you mean?"

"Sam can't get out unless someone goes in. He can get out once the portal's open, and he can bring anyone out with him."

McCoy rolled his eyes, gesturing with his fork as he spoke. "Ok, I get that part of it, but what I don't understand is why I have to go. I am not going inside a damned computer!"

"Bones, he's been in there for five days. He could probably use a doctor to check him out. None of the rest of us are qualified, and we're needed on the outside to monitor and operate the computer and the laser." He grinned, despite his best friend's heavy scowl. "I would love to go down there; in fact, I want Sam to take me down there before we ship out. But I can't because I'm the hacker."

McCoy stared at him levelly, eyes narrowed as he scowled. "You're not going to quit on this, are you?"

Kirk's grin got that much wider. "Nope!"

He was treated to an eye roll. "Fine, I'll do it."

* * *

><p>Everything was ready, Sam had been informed of their plan, and despite McCoy's frequent complaints, he was seated in front of the computer, with the laser at his back, which he was not at all comfortable with, while Jim brought the activation screen he'd come across earlier.<p>

"Everything will be fine, Bones, I promise. All you need to do is tap this button and you're in. Sam's on the other side waiting for you, and you'll be back here in no time." McCoy glared fiercely, not happy at all, despite his agreement.

"Yeah, I got it. Let's just get this over with, alright?" He shoved Jim out of the way and jabbed at the keyboard and he heard the laser power up behind him and he clenched his eyes shut, flinching as a hand touched his shoulder.

He blinked, realizing right away that it was too quiet for the engineering lab. He looked up and saw a young man, probably late 20s, looking at him cautiously. He was wearing clothes McCoy had never seen before, glowing armour and a black jumpsuit. Blond hair like Jim, blue eyes in hallowed cheeks, black bruises accentuating the light color. The kid looked like he hadn't slept, or eaten much.

"Are you Sam Flynn?"

The kid nodded, and McCoy realized there were two other people in the room, wherever he was. The first was rather imposing, solid and dangerous, with more armour than Sam had that glowed with lines of blue and a horrible scar on his face. He looked remarkable like the only picture he'd come across of Alan Bradley, brown hair lightly playing in his hard eyes. The other person in the room kind of looked like Sam, with darker hair.

"Yeah, I'm Sam Flynn. You the doctor Jim promised?"

McCoy nodded, rising to his feet. He extended his hand in greeting. "Yeah, I'm Leonard McCoy, CMO of the Enterprise. You look like shit, kid; when was the last time you slept?"

The Sam lookalike tried to smother his abrupt laugh behind his gloved hand as Sam half-heartedly attempted to glare. Kid was an amateur.

"Actually, not in a while. Been kinda fightin' a war in here." Sam straightened, rising to his full height as he turned and headed for the door. "Gemini will get you set up with an identity disk and proper clothes for while you're here. Before we leave, I have to finish a few things, like finalising a contract for a permanent ceasefire. Come on up when you're done."

McCoy stared in disbelief as the kid and other male left the room, which had no windows, he noticed absently. He cocked his head at the lookalike with a raised eyebrow, hoping his innate cynicism shone through clearly. "So, I guess I hit a nerve?"

Gemini shrugged, offering a faint smile. "It has been rather frantic since my creator arrived here a few hundred cycles ago. Users aren't really welcome right now, and some of the other programs in the city would rather see Sam dead, just for being a User, let alone being the Son of Flynn."

There was so much more to the story than McCoy was getting, and it was starting to bother him. He resolved to learn to whole story in its entirety at some point. "What's this disk he mentioned, and what's wrong with my clothes?"

Gemini lightly put a hand on McCoy's back, manoeuvring the doctor towards a door he hadn't seen before, like it appeared out of nowhere. The room inside was dark, but lights from somewhere in the floor revealed what looked like a human sized incubation tube. So far, this did not look promising.

"Your current attire leaves you fairly noticeable to the natives. You would be attacked on sight so it is my job to provide you with something more inconspicuous. Please, step up." Gemini motioned to the tube as the glass retracted into the floor.

McCoy eyed the device sceptically, but he was on his own here, and he was pretty sure he was safe, mostly because Jim wouldn't have allowed him down here otherwise. If anything happened to him, McCoy was certain that Jim would just trash the computer he was in after getting him out. "Sure, why not?"

He stepped up onto the pad and something clamped down on his feet; he couldn't move. He tensed, waiting the next move but all Gemini did was raise his hands to his shoulders. The tips of the program's fingers lit up and he moved them down McCoy's body, so lightly that the doctor couldn't feel it. He did feel, and saw, when his clothes fell to the floor in pieces, and he was suddenly mostly naked.

He opened his mouth, a diatribe of acerbic expletives more than ready to be let loose, but Gemini smiled at him so disarmingly he faltered and in that moment, the program touched a button next to his feet and something started crawling up his legs, clothing him in a fabric or synthetic he couldn't identify, formfitting but not uncomfortably tight, all the way up to the first inch of his neck.

Gemini stepped away for a few moments, out of McCoy's line of sight, which was actually kind of terrifying, just a little, making his stomach roil in anticipation. Thankfully, Gemini wasn't gone long, but the program has pieces of armour in his arms, and he deftly fitted them to the contours of McCoy's body, his lower legs and upper arms, a belt piece on his hips and another piece on his chest. Once set in place, the pieces started humming, and new armour formed, flickering into existence, connecting it all together, and just like with the others, the armour started glowing, dark blue lines crossing at his ankles and climbing his body. He did notice the shape of his Starfleet badge on his shoulder, the medical cross glowing a bright red and lined with the circuit blue.

"Huh. That's different." This whole process was just baffling. How did this all work?

"Hmm, I haven't seen this color before." Gemini said, lightly tracing one of the blue lines on his arms with his fingers. "Sam said you're a doctor. What exactly does that mean?"

McCoy shrugged, not knowing how to explain what he lived for to someone who may never actually need his skills. "In the simplest sense, I fix people. They come to me with whatever's ailing them, and I fix it."

Really wasn't too much more to what he did.

"In a way, it sounds similar to an antivirus program. You protect your system from infections."

McCoy grinned at the program, who smiled back. "Yeah, that makes sense."

Gemini moved behind him, strapping another, larger, piece or armour to his back. "This is your identity disk; everything you do or learn will be imprinted on this disk. This disk will be everything you are inside the Grid."

He attached something, presumably the disk he mentioned, to the armour on his back, and McCoy blinked as his vision blurred and he felt a connection to the disk on his back.

"Identity disk is activated and synced. Ready to see the Grid?" Gemini released him from the pad and McCoy stumbled, regaining his equilibrium quickly. He looked at Gemini, taking in the firm jaw, the quiet strength hidden beneath the suit, the gleam in those dark eyes, so similar but so different from Flynn, and McCoy liked what he saw, so he nodded, lips quirking into a facsimile of a smile, so very rare in the outside world, but so easy in the program's presence.

"Yeah, show me your world." Gemini grinned at his words, grabbing his hand to lead him up the stairs and into a large room filled with people, although McCoy can clearly see the massive artillery lined up against the windows, and the damage of wear and tear. There were at least a dozen people milling about, most of them surrounding a table in the middle of the room with Sam and the other male.

"Glad you could join us, doctor." Sam said without actually looking back at him. "You're just in time, the remainder of CLU's forces have agreed to a ceasefire on the condition that I create a place for them, kept away from Users."

"Glad things are workin' for you, kid." McCoy moved closer, taking in the advanced holographic displays, the strangeness of the programs in the room. Everything was so different, so strange to him; he was way out of his depth here. He was concerned about the kid; he could see the exhaustion just waiting to knock him out.

Without a more intimate or detailed physical examination, McCoy couldn't be completely sure, but if what Gemini had implied, and what Sam hadn't outright said was true, then Sam had been going on adrenaline and very little else since he got here. He was too skinny, gaunt in the face and around the eyes, reminding McCoy of Jim during finals week at the Academy.

It didn't escape his notice that Sam was relying on the other male; the one with the scar, keeping the program close, and anyone else would have missed the subtle hand keeping Sam from swaying, and undoubtedly giving the kid something to focus on.

McCoy didn't think it was anything too serious, at most just a case of dehydration, malnutrition and exhaustion. Easily fixable, wouldn't take too long, if he could pull the kid away from whatever he was doing here. Oh, McCoy knew the kid's work was important, he just didn't care.

"You gonna be finished up here soon?" He asked, aware of the looks he was getting from some of the other people (programs?) in the room. It made him feel awkward, but he took a small amount of comfort in Gemini's presence beside him.

Wait a minute, yeah, Gemini still had his hand. He really wasn't concerned over that fact, though.

Sam looked up from the map, meeting McCoy's eyes. "I shouldn't be more than an hour, unless you feel otherwise."

So the kid knew he wasn't in good shape. That was good, in McCoy's eyes, but an hour longer couldn't hurt, so he shook his head. "Nah, finish up. You need Gemini for that hour?"

The kid had the nerve to actually smirk at him, though he couldn't figure out why. "Nope, feel like giving a tour, Gemini?"

The program in question grinned, wide and bright like Jim, before pulling him along out of the door, to a world that McCoy never could have imagined. He stuttered to a halt mere feet outside, staring at the massive landscape before him. There was more than just a city in here, this world was amazing, stunning to behold in its dark majesty. Towering skyscrapers, sleek in their design, backlit by roiling lightning, a turbulent storm that never truly broke. Beyond what he could see of the city, which itself was immense on a scale he found staggering, were vast barren plains, stretching out for miles and before the first hints of sharp-edged mountains could be seen in the gloom of the forever-night.

"Come on, let's go for a ride."

McCoy turned away from the epic scenery to frown at Gemini in confusion. "Huh?" Yeah, that was eloquent.

"You just stay right there." The program offered a reassuring grin before moving about a dozen feet away. McCoy saw him pull something thin, a baton, from his waist and start running. Still a few feet away from McCoy he leapt headfirst into the air, holding the baton in front of him and snapping it apart.

A stunning display of pixels and circuits formed in midair under Gemini's body, bright blue and white, solidifying into a kind of motorcycle McCoy had never seen before, compact but sleek and curvy, a stream of light flowing behind.

And very, very fast.

Gemini pulled a sharp u-turn before he was too far away, quickly slowing to a stop in front of McCoy, a wild grin lighting up his face behind the visor. If he hadn't been best friends with Jim for as long as he had, McCoy would have already fled for the relative safety of the arcade, but as it was, he was used to Jim's adrenaline junkie ways, so he could handle this.

His own grin was crooked, roguish as he leered. "You better show me the best you've got, kid."

"I can give you the ride of your life, doctor."

Somehow McCoy didn't think Gemini meant the lightcycle ride.

* * *

><p>AN: As always, feel free to leave a review, I love hearing your opinions. This chapter didn't want to end, not really, but this is a good spot.


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